Soil drying procedure affects the DNA quantification of Lactarius vinosus but does not change the fungal community composition

Drying soil samples before DNA extraction is commonly used for specific fungal DNA quantification and metabarcoding studies, but the impact of different drying procedures on both the specific fungal DNA quantity and the fungal community composition has not been analyzed. We tested three different dr...

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Detalles Bibliográficos
Autores: Castaño Soler, Carles, Parladé Izquierdo, Xavier, Pera i Álvarez, Joan, Martínez de Aragón, Juan, Alday, Josu G., Bonet Lledos, José Antonio
Tipo de recurso: artículo
Estado:Versión aceptada para publicación
Fecha de publicación:2016
País:España
Institución:Universitat de Lleida (UdL)
Repositorio:Repositori Obert UdL
OAI Identifier:oai:repositori.udl.cat:10459.1/63105
Acceso en línea:https://doi.org/10.1007/s00572-016-0714-3
http://hdl.handle.net/10459.1/63105
Access Level:acceso abierto
Palabra clave:Drying treatment
Ectomycorrhizal biomass
Fungal community
qPCR
Metabarcoding
Lactarius
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spelling Soil drying procedure affects the DNA quantification of Lactarius vinosus but does not change the fungal community compositionCastaño Soler, CarlesParladé Izquierdo, XavierPera i Álvarez, JoanMartínez de Aragón, JuanAlday, Josu G.Bonet Lledos, José AntonioDrying treatmentEctomycorrhizal biomassFungal communityqPCRMetabarcodingLactariusDrying soil samples before DNA extraction is commonly used for specific fungal DNA quantification and metabarcoding studies, but the impact of different drying procedures on both the specific fungal DNA quantity and the fungal community composition has not been analyzed. We tested three different drying procedures (freeze-drying, oven-drying, and room temperature) on 12 different soil samples to determine (a) the soil mycelium biomass of the ectomycorrhizal species Lactarius vinosus using qPCR with a specifically designed TaqMan® probe and (b) the fungal community composition and diversity using the PacBio® RS II sequencing platform. Mycelium biomass of L. vinosus was significantly greater in the freeze-dried soil samples than in samples dried at oven and room temperature. However, drying procedures had no effect on fungal community composition or on fungal diversity. In addition, there were no significant differences in the proportions of fungi according to their functional roles (moulds vs. mycorrhizal species) in response to drying procedures. Only six out of 1139 operational taxonomic units (OTUs) had increased their relative proportions after soil drying at room temperature, with five of these OTUs classified as mould or yeast species. However, the magnitude of these changes was small, with an overall increase in relative abundance of these OTUs of approximately 2 %. These results suggest that DNA degradation may occur especially after drying soil samples at room temperature, but affecting equally nearly all fungi and therefore causing no significant differences in diversity and community composition. Despite the minimal effects caused by the drying procedures at the fungal community composition, freeze-drying resulted in higher concentrations of L. vinosus DNA and prevented potential colonization from opportunistic species.This work was supported by a STSM Grant from COST Action FP1203 and by the Spanish Ministry of Economy and Competitivity (MINECO) through the project AGL 2012-40035-C03. Carles Castaño received support from the Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya through the program of Doctorats Industrials, funded by the European Union and the European Social Fund. Josu G. Alday was supported by Juan de la Cierva fellowships (IJCI-2014-21393).Springer-Verlag2016info:eu-repo/semantics/articleinfo:eu-repo/semantics/acceptedVersionhttps://doi.org/10.1007/s00572-016-0714-3http://hdl.handle.net/10459.1/63105reponame:Repositori Obert UdL instname:Universitat de Lleida (UdL)Inglésinfo:eu-repo/grantAgreement/MINECO//AGL2012-40035-C03-01info:eu-repo/grantAgreement/MINECO//AGL2012-40035-C03-03Versió postprint del document publicat a https://doi.org/10.1007/s00572-016-0714-3Mycorrhiza, 2016, vol. 26, núm. 8, p. 799–808(c) Springer-Verlag Berlin Heidelberg, 2016info:eu-repo/semantics/openAccessoai:repositori.udl.cat:10459.1/631052026-06-24T12:42:17Z
dc.title.none.fl_str_mv Soil drying procedure affects the DNA quantification of Lactarius vinosus but does not change the fungal community composition
title Soil drying procedure affects the DNA quantification of Lactarius vinosus but does not change the fungal community composition
spellingShingle Soil drying procedure affects the DNA quantification of Lactarius vinosus but does not change the fungal community composition
Castaño Soler, Carles
Drying treatment
Ectomycorrhizal biomass
Fungal community
qPCR
Metabarcoding
Lactarius
title_short Soil drying procedure affects the DNA quantification of Lactarius vinosus but does not change the fungal community composition
title_full Soil drying procedure affects the DNA quantification of Lactarius vinosus but does not change the fungal community composition
title_fullStr Soil drying procedure affects the DNA quantification of Lactarius vinosus but does not change the fungal community composition
title_full_unstemmed Soil drying procedure affects the DNA quantification of Lactarius vinosus but does not change the fungal community composition
title_sort Soil drying procedure affects the DNA quantification of Lactarius vinosus but does not change the fungal community composition
dc.creator.none.fl_str_mv Castaño Soler, Carles
Parladé Izquierdo, Xavier
Pera i Álvarez, Joan
Martínez de Aragón, Juan
Alday, Josu G.
Bonet Lledos, José Antonio
author Castaño Soler, Carles
author_facet Castaño Soler, Carles
Parladé Izquierdo, Xavier
Pera i Álvarez, Joan
Martínez de Aragón, Juan
Alday, Josu G.
Bonet Lledos, José Antonio
author_role author
author2 Parladé Izquierdo, Xavier
Pera i Álvarez, Joan
Martínez de Aragón, Juan
Alday, Josu G.
Bonet Lledos, José Antonio
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv Drying treatment
Ectomycorrhizal biomass
Fungal community
qPCR
Metabarcoding
Lactarius
topic Drying treatment
Ectomycorrhizal biomass
Fungal community
qPCR
Metabarcoding
Lactarius
description Drying soil samples before DNA extraction is commonly used for specific fungal DNA quantification and metabarcoding studies, but the impact of different drying procedures on both the specific fungal DNA quantity and the fungal community composition has not been analyzed. We tested three different drying procedures (freeze-drying, oven-drying, and room temperature) on 12 different soil samples to determine (a) the soil mycelium biomass of the ectomycorrhizal species Lactarius vinosus using qPCR with a specifically designed TaqMan® probe and (b) the fungal community composition and diversity using the PacBio® RS II sequencing platform. Mycelium biomass of L. vinosus was significantly greater in the freeze-dried soil samples than in samples dried at oven and room temperature. However, drying procedures had no effect on fungal community composition or on fungal diversity. In addition, there were no significant differences in the proportions of fungi according to their functional roles (moulds vs. mycorrhizal species) in response to drying procedures. Only six out of 1139 operational taxonomic units (OTUs) had increased their relative proportions after soil drying at room temperature, with five of these OTUs classified as mould or yeast species. However, the magnitude of these changes was small, with an overall increase in relative abundance of these OTUs of approximately 2 %. These results suggest that DNA degradation may occur especially after drying soil samples at room temperature, but affecting equally nearly all fungi and therefore causing no significant differences in diversity and community composition. Despite the minimal effects caused by the drying procedures at the fungal community composition, freeze-drying resulted in higher concentrations of L. vinosus DNA and prevented potential colonization from opportunistic species.
publishDate 2016
dc.date.none.fl_str_mv 2016
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/acceptedVersion
format article
status_str acceptedVersion
dc.identifier.none.fl_str_mv https://doi.org/10.1007/s00572-016-0714-3
http://hdl.handle.net/10459.1/63105
url https://doi.org/10.1007/s00572-016-0714-3
http://hdl.handle.net/10459.1/63105
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv info:eu-repo/grantAgreement/MINECO//AGL2012-40035-C03-01
info:eu-repo/grantAgreement/MINECO//AGL2012-40035-C03-03
Versió postprint del document publicat a https://doi.org/10.1007/s00572-016-0714-3
Mycorrhiza, 2016, vol. 26, núm. 8, p. 799–808
dc.rights.none.fl_str_mv (c) Springer-Verlag Berlin Heidelberg, 2016
info:eu-repo/semantics/openAccess
rights_invalid_str_mv (c) Springer-Verlag Berlin Heidelberg, 2016
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Springer-Verlag
publisher.none.fl_str_mv Springer-Verlag
dc.source.none.fl_str_mv reponame:Repositori Obert UdL
instname:Universitat de Lleida (UdL)
instname_str Universitat de Lleida (UdL)
reponame_str Repositori Obert UdL
collection Repositori Obert UdL
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,811543

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